To analyze the mechanism by which mustard essential oil nanoemulsion containing citrus pectin and Tween-80(MEO-NE-PT) inhibits the growth of citrus sour rot pathogen, transcriptome sequencing was performed on the mycelia of Geotrichum candidum not treated (control) and treated with 64 μL/L MEO-NE-PT for 4 hours. A total of 2788 differentially expressed genes (DEGs) were identified, including 1364 significantly upregulated and 1424 significantly downregulated genes. These DEGs were significantly enriched in pathways including amino sugar and nucleotide sugar metabolism, steroid biosynthesis, glyoxylate and dicarboxylate metabolism, starch and sucrose metabolism, and ABC transporters. They could synergistically disrupt cellular structure and function and the energy supply, and weaken the pathogen's ability to expel exogenous toxic substances outside the cell. This study provides a scientific basis for the development of eco-friendly preservatives for citrus fruits.